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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAATCCAGTTGCGTATGACATCGCTAATCATTTCTGCGAGATGGCAGCAGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaaatactaccaatgcgctgttttgcttatgttttggtacttaaatcagtttacacaatcttggtccaccttgcttatttgctattctacatgtggcag

Basic information

species Oryza sativa
transcript LOC_Os01g51920.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51920.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G425249_T01 (Zea mays), 5'ss of exon 4
TTCAATCCAGTTGCGTATGACATCGCTAATCATTTCTGCGAGATGGCAGCAGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtac-------ccaaaaatactaccaatgc-------gctgttttgcttatgttttggtacttaaatcagtttacacaatcttggtcca--------ccttgcttatttgctattctacat---gtggcag
||||| |||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||||   ||||| |||| |||||||||||| | |||||||||||        | ||    ||| |  ||||       | ||||||  || | ||||  |  |||| |  |||  || ||| ||||| ||        ||||||| |  ||||| ||||      ||| |||
TTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGGACTACAGCAGATATCCAGgtattgcattactaagtgaactgctgatgcatggacagttgtttt-tttttcttttcttctttaatttggttggcaaaatattggttcagttttcagccttgctcacctgctactctattcttcgtgacag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86497719|gb|CI140352.1|CI140352
EST:     AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAG                         ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
genomic: AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
EST: gi|33684238|gb|CF312477.1|CF312477
EST:     AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAG                         ACACTGATGAGC
genomic: AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGC
EST: gi|325494505|gb|JG459029.1|JG459029
EST:     AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAG                         ACACTGATGAGCAGAAGCGTAATGTGAAGACGTACCTAAGCAATTCTG
genomic: AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
EST: gi|58672419|gb|CK061105.1|CK061105
EST:     AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAG                         ACACTGATGAACAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
genomic: AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
EST: gi|33381326|gb|CF196669.1|CF196669
EST:     AGACTATCATTCAGAGAAGCCACATNNACTGGACTACAGTAAATATCCAG                         ACACTGATGANNAGAAGCGTTTTGTGA
genomic: AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTTTGTGA
EST: gi|58588260|gb|CF986568.1|CF986568
EST:     AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAG                         ACACTGATGAACAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
genomic: AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
EST: gi|86500529|gb|CI143162.1|CI143162
EST:     GGACTACAGTAAATATCCAG                         ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
genomic: GGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
EST: gi|86495212|gb|CI137845.1|CI137845
EST:     AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAG                         ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
genomic: AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
EST: gi|33676500|gb|CF304739.1|CF304739
EST:     AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAG                         ACACTGATGAG
genomic: AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAG
EST: gi|86851235|gb|CI312636.1|CI312636
EST:     AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAG                         ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
genomic: AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
EST: gi|33679472|gb|CF307711.1|CF307711
EST:     AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAG                         ACACTGATGAGCAGAAGCGTTT
genomic: AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTT
EST: gi|86496165|gb|CI138798.1|CI138798
EST:     AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAG                         ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
genomic: AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
EST: gi|40488156|gb|BX898760.1|BX898760
EST:     AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAG                         ACACTGATGAACAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
genomic: AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
EST: gi|86500222|gb|CI142855.1|CI142855
EST:     CACATAGACTGGACTACAGTAAATATCCAG                         ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
genomic: CACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
EST: gi|2311781|gb|C27936.1|C27936
EST:     AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAG                         ACACTGATGNGCAGANGCGTTTTGTGANGACGTACCTAAGCAATTCTGTAA
genomic: AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGTAA
EST: gi|33676093|gb|CF304332.1|CF304332
EST:     AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAG                         ACACTGATGATCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG
genomic: AGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 75 (downstream exon)
Score: 53

TTCAATCCAGTTGCGTATGACATCGCTAATCATTTCTGCGAGATGGCAGCAGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaa ... catgtggcagACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAATCCAGTTGCGTATGACATCGCTAATCATTTCTGCGAGATGGCAGCAGACTATCATTCAGAGAAGCCACATAGACTGGACTACAGTAAATATCCAGgtacccaaaaatactaccaatgcgctgttttgcttatgttttggtacttaaatcagtttacacaatcttggtccaccttgcttatttgctattctacatgtggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC